Nyxaros is a clockwise spiral going down; at the top level, the southern curve of the spiral has a lorestone on its south edge - where you engage the first pack of Silent Choir Hounds. If you speak to the talking statue head, you went past it.

After speaking to the talking statue head in Nyxaros, you are ordered to explore the "secret wing" of the complex. The straight hallway going south has a lorestone on its west side (chances are, your right as you head south).

At the start of the "hidden wing" of Nyxaros, you will come across a large room filled with dead Kollossae. Secandra will stop you to talk about the scene, then give back control of your character. Go east (likely left) from the only torture table (a medieval rack) in the room; a lorestone should be visible in a golden-lit alcove.

You may get the final two lorestones in either order, as you may visit both places, but opt to go only one way initially (rescue the Kollossae Council or save the Jottun slaves). This lorestone is in the hallway leading to the slave pens. It is in the square room before entering the tunnel-entrance to the pens proper.

You may get the final two lorestones in either order, as you may visit both places, but opt to go only one way initially (rescue the Kollossae Council or save the Jottun slaves). This lorestone is placed behind the prisoner chained to the massive pillar in the killing chamber.